/*
 * Copyright (c) 2011 Seoul National University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met: redistributions of source code must retain the above copyright
 * notice, this list of conditions and the following disclaimer;
 * redistributions in binary form must reproduce the above copyright
 * notice, this list of conditions and the following disclaimer in the
 * documentation and/or other materials provided with the distribution;
 * neither the name of the copyright holders nor the names of its
 * contributors may be used to endorse or promote products derived from
 * this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * Authors: Jung Ho Ahn  ( gajh@snu.ac.kr )
 *
 */

#ifndef __CONTIGNODE_H__
#define __CONTIGNODE_H__

#include <string>
#include "KmerNode.h"
#include "Node.h"

class ContigNode : public Node
{
  public:
    ContigNode(KmerNode * knode, uint64_t id_);
    ContigNode(uint64_t id_);
    ~ContigNode();

    Node * getPrev(nucleotide_type nucleotide = nt_A) { return prev; }
    Node * getNext(nucleotide_type nucleotide = nt_A) { return next; }

    void setPrev(Node * node, nucleotide_type nucleotide = nt_A) { prev = node; }
    void setNext(Node * node, nucleotide_type nucleotide = nt_A) { next = node; }

    bool isStandalone()  const { return (prev == NULL && next == NULL); }
    uint32_t getLength() const { return length; }
    void fastaDisplay(ostream & out, bool isPalindrome = false);

    static uint64_t fasta_id;

  private:
    Node * prev;
    Node * next;
    Kmer * kmer;

    uint64_t hitcount;
    int    lm_hitcount : 32;
    int    rm_hitcount : 32;
    uint32_t length;
    bool   prepeat : 1;
    bool   nrepeat : 1;
    //bool   valid   : 1;
    bool   isKmerRC: 1;
    string nucleotides;

  friend class Graph;
  friend ostream & operator<<(ostream & out, const ContigNode & k);
};

#endif  // __CONTIGNODE_H__

